Crossed Wires
by Elycat
Summary: The body of the last living Time Lord is a valuable resource. When the Doctor is taken alive by an alien military, Amy and Rory set out to rescue him, but their efforts might not be enough to save him.


Amy and Rory sprinted through the corridors of the Yaxcori ship, ignoring the intruder alarms periodically flooding the stark halls with red light. The chance for stealth had passed, but it didn't matter. The Yaxcori had the Doctor – _their _Doctor – and no force in the universe was going to stop them from coming after him. This time, it was their turn to rescue him.

"He's somewhere in the heart of the ship," Amy gasped. "We should be getting close—oh!" She stopped short, having nearly run into a sealed metal door at the end of the corridor. "They really need some better lighting in this place," she muttered as Rory reached into his pocket for the sonic screwdriver. It was one of the things the Doctor had left behind, one of the things that had tipped them off that something was very wrong when he didn't come back.

Rory took longer to unlock the door than the Doctor would have, but with an admirable minimum of fumbling. With one nervous glance at each other, the young couple stepped through the doorway as it hissed open.

Like the corridors, at first it was too dark to see. Amy gasped and held a hand to her head in sudden pain; the discordant background hum that carried through the entire ship was suddenly much louder, a high dissonant keening. She looked around her, squinting as her eyes adjusted to the darkness. The scans they'd carried out with River on the TARDIS had indicated the Doctor was being held somewhere around here, but… something was wrong.

Rory was thinking much along the same lines, frowning. "This can't be right. This is an engine room."

Amy glanced at the dark, hulking silhouettes of mechanisms along one wall, and then her gaze fell on a glowing cluster of monitors on the opposite wall. A control panel. "Over here. Maybe we can access ship blueprints or something, figure out where they'd be keeping him."

The monitor flickered as she approached it, flashing strings of numbers and what might have been recognizable words. Amy didn't have time to wonder what, if anything, they said before they were gone. "Great. It doesn't even work."

Then static filled the screen and was replaced by the face of an alien man. The Yaxcori general, the man who'd taken the Doctor. Amy stiffened instantly and Rory was at her side, a hand on her shoulder, his other hand hovering reflexively and uselessly at his waist where no sword hung. He knew his wife had a sort of alien gun she'd stolen from one of the Yaxcori guards, but even now he sometimes felt defenseless without a blade close to hand. The Yaxcori were ruthless, or so River had told them once she'd worked out who had captured the Doctor – a race of conquerors who were infamous for the appalling experiments they'd carried out on prisoners of war. Looking at the general's hardened, ruthless face, Amy could believe the stories all too well.

"You," Amy snarled. "Where's the Doctor? What have you done with him?"

The Yaxcori laughed. "Have you turned around yet, human?"

She did, looking the ship's engine up and down, and then turned back and gave him her best glare. "It's just an engine, what are you talking about?"

The general glanced at someone just offscreen. "Brighten the engine room lights for our human visitors, please."

The lights came up. Amy didn't take her narrowed eyes off the Yaxcori until she heard Rory's strangled voice. "Amy, don't… don't look."

She turned and looked anyway, and could not suppress a sudden shriek at the sight that met her eyes. Amy clapped her hands over her mouth, eyes wide with horror, and pressed close against her husband. Rory's hands tightened on her shoulders until his grip almost hurt. They'd found him after all.

It was little surprise they hadn't noticed him at first. The Doctor was so closely entwined with the engine that he seemed a part of it at first. His face, or what was left of it, was partially obscured by the mechanisms that clamped his head in place, his hair tangled in the wires that connected to his skull in a way that Amy did not want to examine too closely. One green eye stared out into the room, wide and glazed and unblinking; his right eye had been gouged out and a rope of twisted-together cables slithered snakelike into the socket. He had an oxygen mask fastened over his nose and mouth that was fed by several tubes, two or three of which entered his mouth and seemed to continue down his throat. The Time Lord's arms were raised slightly from his sides and literally welded to the mechanisms behind him in places where the skin had been stripped away and replaced with metal. In other places, it had been stripped away but not replaced and other alterations were more visible: wires replacing nerves and muscles, slender transparent tubes rerouting veins, metal struts fused to bone. And he did not appear to have both of his legs fully intact, though what remained was so altered that it was difficult to tell where his legs ended and the ship's systems began.

The image was burned indelibly into Amy's mind by the time she managed to tear her eyes away from the horrific sight and bury her face in Rory's shoulder. He wrapped his arms around her tightly and closed his eyes. In all the time he'd spent travelling in the TARDIS, or guarding the Pandorica, he had never seen anything that sickened him like this. The image of the Doctor, maimed and immobilized, remained in his mind as clearly as if his eyes were open. He wanted to throw up.

Both of them were aware of the Yaxcori's soft chuckles behind them, but it took another couple of moments before either of them had recovered enough to turn and face him. When they did, neither pair of eyes was dry, but none the less deadly for it. Amy's hand hardly shook at all as she raised the gun and aimed it, rather pointlessly, at the Yaxcori general's forehead on the screen. She knew it was just an image, and she didn't care. She hadn't wanted to hurt someone this much since the Silence took her Melody away.

Through clenched teeth, all she could manage to get out was a harsh "_Why_."

"A Time Lord," he said. "The last Time Lord living… the greatest power source in the universe. Hundreds upon hundreds of years of exposure to the Time Vortex, all feeding into my ship. My grandchildren's grandchildren will conquer in this ship and it will still fly for centuries before it breaks down." There was a bright light in his eyes, genuine delight at the thought. Amy felt sick.

"Is he…" Rory swallowed. "Is he _conscious? _Can he _feel_ all of this?_"_

"Why should I care?" the general said softly. "Generations of Yaxcori and lesser beings have powered this ship in the past. A bit late to start worrying about how it made them _feel."_

"You strung him up like that," Amy said, her voice shaking, "and you don't even know if he's in pain. You didn't even bother to _check._"

The general paused. "I never said that. I said it didn't matter." There was a cruel, hard look in his eyes. "If you really want an answer, though." He glanced at someone offscreen again. "Activate the pilot's vocal centers."

Behind her, the Doctor started screaming. No, Amy thought; it was beyond screaming, the sound of something in agony enough to drive anyone mad. She had never heard any living creature make a sound like that before, and she never wanted to again. The gun dropped onto the console as, stumbling, she whipped around and hurried to his side. The Doctor remained motionless, his face still expressionless and frozen, but that awful noise still tore from his throat relentlessly – the only outward sign he was able to give of how much he was hurting. Amy's breath caught again, the depth of what had been done to him hitting her _again _even though this time when she turned she'd known what to expect. Her hands hovered over the Doctor's paralyzed, mutilated body without making contact, desperate to comfort him somehow but reluctant to touch because she feared hurting him further. And, if she were honest, because she was repulsed by what she saw, this horrific patchwork fusion of metal and flesh.

The sounds of the Doctor's anguish continued on, hardly muffled by the oxygen mask sealed over his face. The noise bored into Amy's skull.

"Stop," she managed, finally, unable to bear it any longer. "Stop it!"

"Deactivate vocal centers," she heard the general command. And the Doctor fell silent. The discordant keening of the engines went on, an echo of the Doctor's agony. Deprived of his voice, the entire ship screamed for him. Amy shuddered.

"You're not going to keep him here," Rory was saying behind her. "All those things you said about your grandchildren's grandchildren using him, they're not going to happen. Because right here, right _now,_ we're taking him and you can't stop us. You can't get to the engine room in time."

"I can't stop you, but I don't have to," the Yaxcori said calmly. "Your Time Lord is part of the ship now. You can't simply take my pilot without far more expertise and manpower than you have. You're only two humans! What could you possibly do against the most advanced of Yaxcori science?"

Rory snarled wordlessly, his hand once again reaching for a sword that wasn't there. Not that it would have done much good if he'd had one – the general was all the way across the ship, miles of corridors away, untouchable. At least by him and Amy.

His wife was standing next to him now, holding his arm. "We'll save him," she said, her voice icy. "And by the end of this, you will wish you had never been born. Maybe you won't have been. You have no idea what kinds of forces you've brought down on yourself."

"What forces?" the general said, a note of unease entering his voice.

Amy smiled grimly. "My daughter."

As if on cue, an explosion suddenly rocked the ship. Even in the engine room, Amy and Rory could feel the tremors. On the video screen, they could hear alarms suddenly going off and multiple Yaxcori officers talking at once – the general had time for one last glare at the Ponds before he turned away and the video was cut off.

"There's the diversion River promised us," Rory said. "We've got to get him out of here while we've got the chance."

"_How?"_ Amy said, her steely façade cracking a little as she looked at him desperately. "He's _welded_ to that thing, Rory. How do you know we won't just hurt him worse trying to get him out?"

"Worse than the Yaxcori have?" Rory said grimly, and Amy couldn't answer. "We have to try. We can't leave him here like this."

She took a deep breath and nodded. "I'll see if there's any way to… to disconnect him."

Amy slowly walked back over to the Doctor as Rory began running his hands over the console. "Doctor, can you hear me?" She forced herself to look him in the eye and not flinch away from the sight of his ravaged face. "We're all here. Me and Rory and River. We're going to save you, Doctor, I promise. Just hold on, okay?" She reached up to touch the side of his face above his oxygen mask, and the brief moment when her fingertips brushed his skin was like a bomb going off in her head. She stumbled back, her vision actually blacking out for a second, reeling from the sudden flash of that vast agonized consciousness in her mind. Something felt _wrong_ about it.

"Amy? What happened?" Rory turned to her, all concern, and she belatedly realized that she had cried out.

"I'm fine," she said, her voice coming out all high and shaky, and she cleared her throat. "I'm fine," she said more firmly. "He's… Don't touch him, Rory, it… hurts." Her vision became unexpectedly blurred and she blinked to clear it, wiping eyes on the back of her wrist. "Stupid. He's a telepath, he's unguarded and in pain, of _course_ he's going to lash out at anyone who touches him."

Rory looked at her and then at the Doctor for a long moment, his face nearly unreadable even to her, then turned back to the console. "Well, maybe we won't have to touch him to get him out. I think I've figured some of this out. There's some kind of control mechanism here, and maybe if we can break it…"

He prepared to go at it with his bare hands, and before she knew what she was doing Amy had grabbed his arm and bodily dragged him back. "Don't!" she yelped. He stared at her. "You can't, he'd feel it," she babbled, desperately trying to put into words what she'd felt in that brief flash of the Doctor's mind. "He _is_ the ship, Rory, or he's… _in_ the ship, it's not like I thought, he's not just fuel, he's…"

"He's part of the ship," Rory said slowly, his face filling with horrified understanding. "What was it the Yaxcori general called him… the pilot."

For a moment neither of them spoke and the silence was only broken by the engines' keening. The noise drilled into her skull and she wanted to yell and shout and swear to drown it out. He really was screaming, his pain projected through the ship's voice rather than his own.

"River," Amy said numbly. "She's tearing this ship to pieces trying to find him. She doesn't know."

Another explosion thrummed through the ship, and maybe it was a trick of the light, but she thought she saw the Doctor shift slightly and the keening of the engines seemed to intensify. Something in her snapped, and she let out a furious yell. "He's _hurting _and there's no way to get him out!" she shouted hoarsely, whirling on the console and only just restraining herself from slamming a fist down on it.

The screen that the general had used to communicate with them suddenly flickered. "Look," Rory said softly.

Slowly, alien symbols appeared on the screen again, then flickered and resolved themselves into recognizable shapes. Amy and Rory leaned forward.

a2lsbCBtZQ==  
>6b 69 6c 6c 20 6d 65<br>amy

Amy's hands flew to her mouth again, her eyes going wide. Rory looked over his shoulder, then back at the screen, then at his wife, dumbfounded. "Is that…"

Amy lowered her hands to speak, her voice choked. "He's communicating with us." She raised her voice, speaking to the man behind her and never taking her eyes off the screen. "We're here, Doctor. Tell us what to do."

Words and numbers flew across the screen, as if typed impossibly fast.

_am y_  
><em>ro½±ºry<em>  
><em>70 6c 65 61 73 65 20 68 65 6c 70 20 6d 65 20 69 74 20 68 75 72 74 73 20 69 74 20 68 75 72 74 73 20 69 74 20 68 75 72 74 73<em>  
><em>YW15cm9yeQ==pon ds<em>  
><em>kđÇǁµ<em>  
><em>112 108 101 97 32 115 101<em>  
><em>killme<em>

The two clearest words chilled her to the core.

"Kill me," Amy read aloud, so softly that Rory could barely hear her. Convulsively she reached out and gripped his hand tightly.

The text continued to appear on the screen, sometimes slowing, sometimes deteriorating into unreadable characters and strings of digits, but never stopping.

_aĂåæmy r▌orY_  
><em>plZQ==ase<em>  
><em>6b 69 6c 6c 20 6d 65<em>  
><em>kill me<em>  
><em>let¿½ïme d½ie<em>  
><em>i n01100101eed 74 6f 20 67 65 74 20 6f 75 74 20 69<em>  
><em>i¯¢ïm sorry 0111001101101111 73 6f 72 72 79<em>  
><em>69 e2 80 99 6c 6c regŀƏǁneratȾɂe<em>  
><em>ev¾ïrythŦng wilØ be o<em>

The ship rocked in another explosion and the sentence stopped abruptly; Amy and Rory watched as numbers and code suddenly began to scroll across the screen far more rapidly than before.

_73 74 6f 70 20 73 74 6f 70 20 73 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 74 == 72 69 76 65 72 20 77 68 65 72 65 20 61 72 65 20 79 6f 75 20 69 27 6d 20 62 75 72 6e 69 6e 67 Sealing breaches and redirecting power to visual feeds 63 61 4e 27 54 20 53 45 45 20 63 61 6e c3 a2 ef bf bd ef bf bd 74_  
><em>ERR: Central pilotdatabank system overload 49 54 20 48 55 52 54 53 20 4c 45 54 20 4d 45 20 44 49 45 20 4c 45 54 20 4d 45 20 44 49 45_  
><em>VTN_ERR_6039: Unexpected matrix interface disruption<em>  
><em>ERR: Access sealĄ®³¡<em>  
><em>FEEDBACK_OVERLOAD<em>  
><em>Launch diagnostic routine 982<em>  
><em>Warning: sensory failure in SEC_73<em>  
><em>Warning: sensory failure in SEC_89<em>  
><em>Warning: sens¾½¿Æ□□□□0110110001100101011101000110 11010110010101000100 0100100101000101<em>  
><em>61 6d 79 20 72 6f 72 79 20 72 69 76 65 72 20 73 6f 72 72 79 20 69 27 6d 20 73 6f 72 72 79 20 6b 69 6c 6c 20 6d 65 20 6b 69 6c 6c 20 6d 65 20 6b 69 4c 4c 20 4d 45 20 4b 49 4c 4c 20 4d 45 20<em>  
><em>011000010110110101111001<em>  
><em>amŶ½Øþ®¹PlEĄ¾SE<em>

The last lines froze on the screen for several long seconds, flickering, before another blast sent more coding and error messages skidding across the screen almost too fast to see. Amy tore her eyes from the rapidly scrolling digits and slowly turned, forcing herself to look at the mutilated Doctor. He was shaking violently under the strain, his face still horrifyingly blank, as the transparent tubing fed different fluids into his veins.

Heavy, creeping numbness began to replace the horror and nausea. Slowly Amy bent down, picked up the gun she'd dropped earlier, and raised it to point at the Doctor's chest. She stepped forward, hands shaking so badly that she wondered if she'd be able to pull the trigger. "Rory, stand back."

He looked at her in alarm, and stepped forward to grab her arm. "No, Amy," he said.

She turned to look at him, her eyes blank with despair. "He's suffering and we can't save him," she said. "I have to end this."

"No. He wouldn't want this."

"He _told _me what he wanted! You saw!"

"No," Rory repeated, firm. "Not like this. He wouldn't want you to do it. He wouldn't want you to have to live with that."

Slowly, he coaxed the gun out of her shaking fingers and stepped forward until he stood at point-blank range, the gun aimed at the left side of the Doctor's chest. "Remember he has two hearts," Amy whispered, standing close behind him and gripping his free arm with both of her hands.

"I know," Rory said softly. He closed his eyes and taking a deep breath, remembering – _This isn't fair! You're turning me into you!_ He'd never wanted to be the one to make these choices. But… better him than Amy. He and the Doctor both knew that. He pressed the barrel lightly into the Doctor's chest over one of his hearts.

"Doctor, can you hear me?" Amy said quietly. "I'm here, we're both here. It's all right, Doctor." She swallowed past the lump in her throat, her voice shaking badly. "It's going to be okay. Just like you told me that first night, remember? Everything's going to be fine."

And Rory pulled the trigger, shifted his aim, pulled it again.

Alarms began to sing and the noise of the engines stuttered, but Amy didn't hear, turning to wrap her arms around Rory and sobbing into his shoulder. He held her, letting the numbness sweep through him, still staring at the Doctor through damp, reddened eyes.

Then it began, just as both of them had been praying it would, the golden glow beginning to wreathe the Doctor's face and hands. Rory stepped back, pulling Amy with him, and the couple clung together and watched as the regeneration energy swept over the Doctor's mutilated body, bright enough to briefly hide him from view.

It was over almost as soon as it began. The glow faded as if sinking into the machine behind him and left his body behind, unchanged, still lifeless. Amy let go of Rory and stumbled forward, taking the Doctor's face in her hands. This time, there was no psychic backlash, no signs of life at all. "Doctor," she said desperately. "Doctor, please. Don't do this to me again. You can't leave me." She brushed his hair back from his face, her fingers catching on wires, and leaned forward to kiss his forehead. When she pulled back, her face was streaked with tears.

Suddenly, impossibly, she heard his voice. "There we are. Amy? Rory? Can you see me?"

She whipped around; so did Rory. There he stood next to the control console, looking just as he always had. Amy's hands balled into fists and she rushed at him, not sure whether she was going to hit him or kiss him or grab hold and never let go – but as soon as she got to him, she passed straight through him. Shakily, she backed away, staring at him with betrayed disbelief.

"I'm sorry," the Doctor said softly. "This is only a hologram. It won't last, but I wanted a chance to say goodbye properly. I owe the both of you that much."

"You regenerated," Amy said shakily. "I saw you. So why did you – why did you still—"

"The ship absorbed the energy from my regeneration cycle," the Doctor said. "It was _designed_ to feed off living energy. But my regeneration was too much – overloaded it. Technically, this isn't _me_, I'm just a… a remnant, a ghost if you like, preserved in the ship's databanks. I'm already fading, but that's all right. By the time I'm gone, you two will be safely back on the TARDIS and this technology will be destroyed permanently."

"I'm sorry," Rory suddenly said, choking up. "We couldn't save you."

"No," the Doctor said softly, shaking his head. "No, no, no. You did save me. I was dying from the moment they put me in there, Rory, and it would have taken hundreds upon hundreds of years for it to end. You saved me from that, and I thank you… and I'm sorry." He looked from Rory to Amy and back again, seeming to drink in the images of his companions, committing them to memory. "I'm so sorry to have put you through this. You deserve so much more than me."

"Wouldn't have given up a thing," Amy whispered. "Not for the world."

The Doctor smiled, a small, sincere half-smile as he gazed at the two of them. "Amelia Pond and Rory Williams. Two of the finest people in the universe. You're going to be brilliant. Well. You already have been." He shifted his jaw and blinked a few times, looking for a moment as if tears were going to spring to his eyes too, holographic though he was. "And tell River… tell her…"

He couldn't finish. Amy nodded, understanding anyway. "We will."

The Doctor smiled at both of them. Amy's vision blurred again. "Doctor," she started, but suddenly their surroundings shifted and twisted and they were standing on the TARDIS again. He'd taken control of the ship's systems, Amy realized, and teleported them both.

She took Rory's hand silently and led him over to sit by the TARDIS console. For a long time they huddled together beside the warmth of the living machine and mourned, all three of them, in the stillness.


End file.
